Noise reduction on only one layer
I have listed down the steps and attached the implemented blender file here.


Move the red circular object to layer 2
Give a material index to red object. I have given it a value of 1. We do this to have a mask for this object, which will be helpful during compositing.




3.Setup render layers as follows. Notice denoising is checked in render layer with shadow. Also 'material index' pass is checked for red object layer, which we will use in compositing.






In the compositor, set up the nodes as shown below.Basically, the material Id mask cuts out just the red object from the second render layer. We then add this to the other render layer with shadow. 




Done! Checkout the attached blend file, where I implemented the above steps.